Antibody which binds human blue-light photoreceptor hCRY2

ABSTRACT

The present invention relates to a novel member of the blue-light photoreceptor family of receptors. In particular, isolated nucleic acid molecules are provided encoding the human hCRY2 receptor. hCRY2 polypeptides are also provided as are vectors, host cells, antibodies, and recombinant methods for producing the same.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.09/105,254, filed Jun. 26, 1998 (now U.S. Pat. No. 6,569,994), which isa divisional of U.S. application Ser. No. 08/964,268, filed Nov. 4, 1997(now U.S. Pat. No. 6,114,503), which claims benefit under 35 § U.S.C.119(e) of U.S. Provisional Application No. 60/030,189 filed Nov. 4,1996. Each of the above referenced patents and patent applications ishereby incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention relates to a novel human blue-light photoreceptor.More specifically, isolated nucleic acid molecules are provided encodinga human blue-light photoreceptor. Human blue-light photoreceptorpolypeptides are also provided, as are vectors, host cells, antibodies,and recombinant methods for producing the same.

2. Related Art

In many organisms, the photolyase/photoreceptor family of proteinsmediates DNA repair. In plants, certain developmental processes areregulated by blue-light. This regulation occurs by a photoinducedelectron transfer reaction (Taylor, J. S., Acc. Chem. Res. 27:76-82(1994); Menkens, A. E. et al., Biochemistry 34:6892-6899 (1995); Heelis,P. F. et al., Photochem. Photobiol. 95:89-98 (1996); and Sancar A.,Science 272:48-49 (1996)). Indeed, to date, most of the work concerningblue-light photoreceptors has been conducted in plants (Cashmore, A. R.et al., International Patent Application WO 96/01897 (1996); Hinnemann,H., Photochem. Photobol. 61:22-31(1995); Short, T. W. et al., Annu. Rev.Plant. Physiol. Plant Mol. Biol. 45:143-171 (1994); Hohl, N. et al.,Photochem. Photobiol. 55:239-245 (1992)) and fungi (Dunlap, J. C., Annu.Rev. Physiol. 55:683-728 (1993)). In plants, blue-light inducesresponses such as photomorphogenesis, phototropism and hypocotylelongation. In particular, it has been demonstrated that the HY4 gene ofA. thaliana, which encodes the CRY1 protein, is required for blue-lightinduced hypocotyl elongation (Ahmad, M., et al., Nature 366:162-166(1993)).

In animals, most of the work on light response (other than vision) hasbeen concentrated on circadian clocks. In D. melanogaster, two geneshave been cloned, timeless and period, which regulate the circadianrhythm (Myers, M. P. et al., Science 270:805-808 (1995); Gekakis, N. etal., Science 270:811-814 (1995)). Both appear to be transcriptionfactors for which activity is regulated by light. A mutation in thegolden hamster tau gene disrupts the circadian clock (Ralph and Menaker,1988). Three mouse genes, CLOCK, ICER, and CREM, which are involved inthe control of circadian rhythm, have been investigated in some detail(Vitaterna et al., M. H. et al., Science 264:719-725 (1994);Sassone-Corsi, P. A., Rev. Cell Dev. Biol. 11:355-377 (1995); Foulkes,N. S. et al., Nature 381:83-85 (1996)). Each of these three geneproducts appears to be a transcriptional repressor for which activity isregulated by light. However, how the light signal is transmitted tothese transcriptional regulators is not known.

Currently, the photolyase/photoreceptor protein family is known tocontain three members: the cyclobutane pyrimidine dimer (Pyr<>Pyr)photolyase (photolyase), the (6-4) photolyase, and the blue-lightphotoreceptor (Todo, T. et al., Science 272:109-112 (1996)). The genefor the classical Pyr<>Pyr photolyase has been cloned and the enzyme hasbeen purified from many organisms, including Escherichia coli,Saccharomyces cerevisiae, Drosophila melanogaster, and Carassius auratus(Sancar, A., Mutation Res. 236:147-160(1990); Kato, T. et al., Nucl.Acids Res. 22:4119-4124 (1994); and Yasui, A. et al., EMBO J.13:6143-6151 (1994). The (6-4) photolyase has been found in D.melanogaster (Todo, T. et al., Nature 361:371-374 (1993); Kim, S. T. etal., J. Biol. Chem. 269:8535-8540 (1994)), Xenopus laevis, and Crotalusatrox (Kim, S. T. et al., Photochem. Photobiol. 63:292-295 (1996)).

Concerning the cloning of (6-4) photolyase genes, only the Drosophilagene has been cloned and sequenced (Todo, T. et al., Science 272:109-112(1996)). The genes for the apoproteins of the blue-light photoreceptorsof Arabidopsis thaliana (Ahmad, M., Nature 366:162-166 (1993)), Sinapisalba (Batschauer, A., Plant J. 4:705-709 (1993); Malhotra, K. et al.,Biochemistry 34:6892-6899 (1995)), and Chlamydomonas reinhardtii (Small,G. D., et al., Plant Molec. Biol. 28:433-454 (1995)) have been clonedand sequenced. The photoreceptors of A. thaliana (Malhotra, K. et al.,Biochemistry 34:6892-6899 (1995); Lin, C. et al., Science 269: 968-970(1995)) and S. alba (Malhotra, K. et al., Biochemistry 34:6892-6899(1995)) have been purified and characterized.

Circadian regulation of human and animal physiology, and particularlycircadian regulation mediated by blue-light photoreceptors, is poorlyunderstood. Thus, there is a need for an isolated human blue-lightphotoreceptor gene, the polypeptide encoded by that gene, and antibodiesspecific for that polypeptide.

SUMMARY OF THE INVENTION

The present invention provides isolated nucleic acid moleculescomprising a polynucleotide encoding the human blue-light photoreceptorhCRY2 [hereinafter “hCRY2”] receptor having the amino acid sequenceshown in SEQ ID NO:2 or the amino acid sequence encoded by the cDNAclone deposited in a bacterial host as ATCC Deposit Number 97769 on Oct.22, 1996.

The present invention also relates to recombinant vectors, which includethe isolated nucleic acid molecules of the present invention, to hostcells containing the recombinant vectors, to host cells containing anisolated polypeptide, as well as to methods of making such vectors andhost cells and for using them for production of hCRY2 polypeptides orpeptides by recombinant techniques.

The invention further provides an isolated hCRY2 polypeptide having anamino acid sequence encoded by a polynucleotide described herein.

The invention further provides isolated antibodies that bindspecifically to the full length hCRY2 receptor, the mature hCRY2receptor, the hCRY2 receptor extracellular domain, the hCRY2 receptortransmembrane domain, the hCRY2 receptor intracellular domain, andepitope-bearing portions of the hCRY2 receptor.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1E show the nucleotide (SEQ ID NO:1) and deduced amino acid(SEQ ID NO:2) sequences of hCRY2 receptor. The protein has a predictedleader sequence of about 22 amino acid residues (underlined) and adeduced molecular weight of about 81 kDa. It is further predicted thatamino acid residues from about 23 to about 514 (about 1 to about 492 inSEQ ID NO:2) constitute the extracellular domain; from about 515 toabout 527 (about 493 to about 505 in SEQ ID NO:2) the transmembranedomain; and from about 528 to about 593 (about 506 to about 571 in SEQID NO:2) the intracellular domain.

FIG. 2 shows the regions of similarity between the amino acid sequencesof the hCRY2 receptor protein and hCRY1 (SEQ ID NO:3).

FIG. 3 shows an analysis of the hCRY2 receptor amino acid sequence.Alpha, beta, turn and coil regions; hydrophilicity and hydrophobicity;amphipathic regions; flexible regions; antigenic index and surfaceprobability are shown. In the “Antigenic Index—Jameson-Wolf” graph,amino acid residues about 30 to about 39, about 45 to about 52, about 77to about 92, about 96 to about 103, about 158 to about 169, about 178 toabout 187, about 253 to about 261, about 293 to about 301, about 320 toabout 331, about 338 to about 346, about 350 to about 356, about 437 toabout 448, and about 534 to about 541 in FIG. 1 correspond to the shownhighly antigenic regions of the hCRY2 receptor protein. These highlyantigenic fragments in FIG. 1 correspond to the following fragments,respectively, in SEQ ID NO:2: amino acid about 8 to about 17, about 23to about 30, about 55 to about 70, about 74 to about 81, about 136 toabout 147, about 156 to about 165, about 231 to about 239, about 271 toabout 279, about 298 to about 309, about 316 to about 324, about 328 toabout 334, about 415 to about 426, and about 512 to about 519.

FIGS. 4A-4C shows the sequence comparison of E. coli photolyase (E.c.)(SEQ ID NO:4), Arabidopsis HY4 photoreceptor (A.t.) (SEQ ID NO:5),Drosophila melanogaster (6-4) photolyase (D.m.) (SEQ ID NO:6), and thehuman blue-light photoreceptors hCRY1 (SEQ ID NO:3) and hCRY2 (SEQ IDNO:2). Amino acid residues which are identical in the entire set areboxed.

FIG. 5 shows the maps of plasmids pDH1996-1 and pDH1996-2, which wereused to express hCRY1 and hCRY2, respectively, as maltose binding fusionproteins. PDH1996-1 contains the hCRY1 cDNA. pDH1996-2 contains thehCRY2 cDNA. The arrows indicate the length and direction oftranscription of the maltose binding protein (malE), blal, andphotoreceptor genes.

FIGS. 6A-6C shows the absorption and fluorescence spectra of hCRY1 andhCRY2 MBP fusion proteins. The dashed line represents the spectra ofhCRY1 and the solid line represents the spectra of hCRY2. (A) Absorptionspectra. (B) Fluorescence excitation and emission spectra of the hCRY1and hCRY2 chromophores at pH 2. Fluorescence excitation spectra wererecorded by monitoring emission at 520 nm. Fluorescence emission spectrawere recorded by using excitation at 450 nm. (C) Fluorescence excitationand emission spectra of hCRY1 and hCRY2 chromophores at pH 10.Fluorescence excitation spectra were recorded by monitoring emission at470 nm. Fluorescence emission spectra were recorded by using 380 nmexcitation.

DETAILED DESCRIPTION

The present invention provides isolated nucleic acid moleculescomprising a polynucleotide encoding a hCRY2 polypeptide having theamino acid sequence shown in SEQ ID NO:2. The amino acid sequence wasdeduced from the sequence of a cloned hCRY2 cDNA. The sequenced cDNAclone was obtained using RACE-PCR (infra). The hCRY2 protein of thepresent invention shares sequence homology with hCRY1 (FIG. 2; SEQ IDNO:3).

A cDNA encoding a maltose binding protein-hCRY2 fusion protein,including amino acid residues −15 to 571 (SEQ ID NO:2) was deposited onOct. 22, 1996 at the American Type Culture Collection, PatentDepository, 10801 University Boulevard, Manassas, Va. 20110-2209, andgiven accession number 97769. The hCRY2 sequence is contained betweenthe EcoR V and Hind III sites in the polylinker of the Mal-C2 vector(NEB, Beverly, Mass.).

Nucleic Acid Molecules

Unless otherwise indicated, all nucleotide sequences determined bysequencing a DNA molecule herein were determined using an automated DNAsequencer (such as the Model 373 from Applied Biosystems, Inc.), and allamino acid sequences of polypeptides encoded by DNA molecules determinedherein were predicted by translation of a DNA sequence determined asabove. Therefore, as is known in the art for any DNA sequence determinedby this automated approach, any nucleotide sequence determined hereinmay contain some errors. Nucleotide sequences determined by automationare typically at least about 90% identical, more typically at leastabout 95% to at least about 99.9% identical to the actual nucleotidesequence of the sequenced DNA molecule. The actual sequence can be moreprecisely determined by other approaches including manual DNA sequencingmethods well known in the art. As is also known in the art, a singleinsertion or deletion in a determined nucleotide sequence compared tothe actual sequence will cause a frame shift in translation of thenucleotide sequence such that the predicted amino acid sequence encodedby a determined nucleotide sequence will be completely different fromthe amino acid sequence actually encoded by the sequenced DNA molecule,beginning at the point of such an insertion or deletion.

Using the information provided herein, such as the nucleotide sequencein SEQ ID NO:1, a nucleic acid molecule of the present inventionencoding a hCRY2 polypeptide may be obtained using standard cloning andscreening procedures, such as those for cloning cDNAs using mRNA asstarting material. Illustrative of the invention, the nucleic acidmolecule described in SEQ ID NO:1 was discovered in a cDNA libraryderived from human fetal brain. The hCRY2 gene was also identified incDNA libraries from the following tissues: synovial sarcoma, restingT-cell, infant brain, cerebellum, endometrial tumor, testes tumor, adultretina, chondrosarcoma, breast, and pituitary.

The determined nucleotide sequence of the hCRY2 cDNA of SEQ ID NO:1contains an open reading frame encoding a protein of about 593 aminoacid residues, with a predicted leader sequence of about 22 amino acidresidues, and a deduced molecular weight of about 81 kDa. The hCRY2protein shown in SEQ ID NO:2 is about 74% identical and about 85%similar to hCRY1 (FIG. 2; SEQ ID NO:3).

As indicated, the present invention also provides the mature form(s) ofthe hCRY2 receptor of the present invention. According to the signalhypothesis, proteins secreted by mammalian cells have a signal orsecretory leader sequence which is cleaved from the mature protein onceexport of the growing protein chain across the rough endoplasmicreticulum has been initiated. Most mammalian cells and even insect cellscleave secreted proteins with the same specificity. However, in somecases, cleavage of a secreted protein is not entirely uniform, whichresults in two or more mature species on the protein. Further, it haslong been known that the cleavage specificity of a secreted protein isultimately determined by the primary structure of the complete protein,that is, it is inherent in the amino acid sequence of the polypeptide.Therefore, the present invention provides a nucleotide sequence encodingthe mature hCRY2 polypeptides having the amino acid sequence encoded bythe cDNA clone contained in the host identified as ATCC Deposit No.97769and as shown in SEQ ID NO:2. By the mature hCRY2 protein having theamino acid sequence encoded by the cDNA clone contained in the hostidentified as ATCC Deposit 97769 is meant the mature form(s) of thehCRY2 receptor produced by expression in a mammalian cell (e.g., COScells, as described below) of the open reading frame encoded by thehuman DNA sequence of the clone contained in the vector in the depositedhost. This clone lacks amino acid residues −22 to −16 in SEQ ID NO:2. Asindicated below, the mature hCRY2 receptor having the amino acidsequence encoded by the cDNA clone contained in ATCC Deposit No.97769may or may not differ from the predicted “mature” hCRY2 protein shown inSEQ ID NO:2 (amino acids from about 1 to about 571) depending on theaccuracy of the predicted cleavage site.

Methods for predicting whether a protein has a secretory leader as wellas the cleavage point for that leader sequence are available. Forinstance, the methods of McGeoch (Virus Res. 3:271-286 (1985)) and vonHeinje (Nucleic Acids Res. 14:4683-4690 (1986)) can be used. Theaccuracy of predicting the cleavage points of known mammalian secretoryproteins for each of these methods is in the range of 75-80%. vonHeinje, supra. However, the two methods do not always produce the samepredicted cleavage point(s) for a given protein.

In the present case, the predicted amino acid sequence of the completehCRY2 polypeptide of the present invention was analyzed by a computerprogram (“PSORT”) (K. Nakai and M. Kanehisa, Genomics 14:897-911(1992)), which is an expert system for predicting the cellular locationof a protein based on the amino acid sequence. As part of thiscomputational prediction of localization, the methods of McGeoch and vonHeinje are incorporated. The analysis by the PSORT program predicted thecleavage sites between amino acids 27 and 28 in SEQ ID NO:2. However,based on homology to the hCRY1 protein (FIG. 2; SEQ ID NO:3), thecleavage site is predicted to be between amino acids −1 and 1 in SEQ IDNO:2. Thus, the leader sequence for the hCRY2 protein is predicted toconsist of amino acid residues −1 to −22 in SEQ ID NO:2, while themature hCRY2 protein is predicted to consist of amino acids residues1-571 in SEQ ID NO:2.

As one of ordinary skill would appreciate, however, due to thepossibilities of sequencing errors, as well as the variability ofcleavage sites for leaders in different known proteins, the full-lengthhCRY2 polypeptide comprises about 593 amino acids, but may be anywherein the range of about 580 to about 600 amino acids; and the leadersequence is about 22 amino acids, but may be anywhere in the range ofabout 15 to about 55 amino acids.

As indicated, nucleic acid molecules of the present invention may be inthe form of RNA, such as mRNA, or in the form of DNA, including, forinstance, cDNA and genomic DNA obtained by cloning or producedsynthetically. The DNA may be double-stranded or single-stranded.Single-stranded DNA or RNA may be the coding strand, also known as thesense strand, or it may be the non-coding strand, also referred to asthe anti-sense strand.

By “isolated” nucleic acid molecule(s) is intended a nucleic acidmolecule, DNA or RNA, which has been removed from its native environmentFor example, recombinant DNA molecules contained in a vector areconsidered isolated for the purposes of the present invention. Furtherexamples of isolated DNA molecules include recombinant DNA moleculesmaintained in heterologous host cells or purified (partially orsubstantially) DNA molecules in solution. Isolated RNA molecules includein vivo or in vitro RNA transcripts of the DNA molecules of the presentinvention. Isolated nucleic acid molecules according to the presentinvention further include such molecules produced synthetically.

Isolated nucleic acid molecules of the present invention include DNAmolecules comprising the open reading frame (ORF) shown in SEQ ID NO: 1;DNA molecules comprising the coding sequence for the mature hCRY2receptor shown in SEQ ID NO:2; and DNA molecules which comprise asequence substantially different from those described above but which,due to the degeneracy of the genetic code, still encode the hCRY2receptor. Of course, the genetic code is well known in the art. Thus, itwould be routine for one skilled in the art to generate such degeneratevariants.

In another aspect, the invention provides isolated nucleic acidmolecules encoding the hCRY2 polypeptide having an amino acid sequenceencoded by the cDNA set forth in SEQ ID NO:1 and by the clone containedin the plasmid deposited as ATCC Deposit No. 97769 on Oct. 22, 1996. Infurther embodiments, this nucleic acid molecule will encode the maturepolypeptide or the full-length polypeptide lacking the N-terminalmethionine. The invention further provides an isolated nucleic acidmolecule having the nucleotide sequence shown in SEQ ID NO:1 or thenucleotide sequence of the hCRY2 receptor cDNA contained in theabove-described deposited clone, or a nucleic acid molecule having asequence complementary to one of the above sequences. Such isolatedmolecules, particularly DNA molecules, are useful as probes for genemapping, by in situ hybridization with chromosomes, and for detectingexpression of the hCRY2 receptor gene in human tissue, for instance, byNorthern blot analysis.

The present invention is further directed to fragments of the isolatednucleic acid molecules described herein. By a fragment of an isolatednucleic acid molecule having the nucleotide sequence of the depositedcDNA or the nucleotide sequence shown in SEQ ID NO:1 is intendedfragments at least about 15 nt, and more preferably at least about 20nt, still more preferably at least about 30 nt, and even morepreferably, at least about 40 nt in length which are useful asdiagnostic probes and primers as discussed herein. Of course, largerfragments 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600,650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250,1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, 1700, or 1750 nt inlength are also useful according to the present invention, as arefragments corresponding to most, if not all, of the nucleotide sequenceof the deposited cDNA or as shown in SEQ ID NO: 1. By a fragment atleast 20 nt in length, for example, is intended fragments which include20 or more contiguous bases from the nucleotide sequence of thedeposited cDNA or the nucleotide sequence as shown in SEQ ID NO:1.

Preferred nucleic acid fragments of the present invention includenucleic acid molecules encoding: a polypeptide comprising the hCRY2receptor extracellular domain (predicted to constitute amino acidresidues from about 1 to about 492 in SEQ ID NO:2); a polypeptidecomprising the hCRY2 receptor transmembrane domain (predicted toconstitute amino acid residues from about 493 to about 505 in SEQ IDNO:2); a polypeptide comprising the hCRY2 receptor intracellular domain(predicted to constitute amino acid residues from about 506 to about 571in SEQ ID NO:2); and a polypeptide comprising the hCRY2 receptorextracellular and intracellular domains with all or part of thetransmembrane domain deleted. As above with the leader sequence, theamino acid residues constituting the hCRY2 receptor extracellular,transmembrane and intracellular domains have been predicted by computeranalysis. Thus, as one of ordinary skill would appreciate, the aminoacid residues constituting these domains may vary slightly (e.g., byabout 1 to about 15 amino acid residues) depending on the criteria usedto define each domain.

Preferred nucleic acid fragments of the present invention also includenucleic acid molecules encoding epitope-bearing portions of the hCRY2receptor protein. In particular, such nucleic acid fragments of thepresent invention include nucleic acid molecules encoding: a polypeptidecomprising amino acid residues from about 8 to about 17 in SEQ ID NO:2;a polypeptide comprising amino acid residues from about 23 to about 30in SEQ ID NO:2; a polypeptide comprising amino acid residues from about55 to about 70 in SEQ ID NO:2; a polypeptide comprising amino acidresidues from about 74 to about 81 in SEQ ID NO:2; a polypeptidecomprising amino acid residues from about 136 to about 147 in SEQ IDNO:2; a polypeptide comprising amino acid residues from about 156 toabout 165 in SEQ ID NO:2; a polypeptide comprising amino acid residuesfrom about 231 to about 239 in SEQ ID NO:2; a polypeptide comprisingamino acid residues from about 271 to about 279 in SEQ ID NO:2; apolypeptide comprising amino acid residues from about 298 to about 309in SEQ ID NO:2; a polypeptide comprising amino acid residues from about316 to about 324 in SEQ ID NO:2; a polypeptide comprising amino acidresidues from about 328 to about 334 in SEQ ID NO:2; a polypeptidecomprising amino acid residues from about 415 to about 426 in SEQ IDNO:2; and a polypeptide comprising amino acid residues from about 512 toabout 519 in SEQ ID NO:2. It is believed that the above polypeptidefragments are antigenic regions of the hCRY2 receptor. Methods fordetermining other such epitope-bearing portions of the hCRY2 protein aredescribed in detail below.

In addition, the present inventors have identified nucleic acidmolecules having nucleotide sequences related to extensive portion ofSEQ ID NO:1 which have been determined from the following related cDNAclones: HFCAD18R (SEQ ID NO:17); HDPFZ96R (SEQ ID NO:18); HBNAG83R (SEQID NO:19); and HJBAZ81R (SEQ ID NO:20). HFCAD18R (SEQ ID NO: 17) isrelated to nucleotides 1372 to 1661 of SEQ ID NO:1. HDPFZ96R (SEQ IDNO:18) is related to nucleotides 611 to 712 of SEQ ID NO:1. HBNAG83R(SEQ ID NO:19) is related to nucleotides 3546 to 3691 of SEQ ID NO:1.HJBAZ81R (SEQ ID NO:20) is related to nucleotides 2460 to 2600 of SEQ IDNO: 1.

The sequence of a public EST, having GenBank Accession No. AA338421,related to a portion of SEQ ID NO:1 is shown in SEQ ID NO:21. Thispublic EST contains a region of 290 nucleotides that are related tonucleotides 1260-1549 of SEQ ID NO:1.

The sequence of another public EST, having GenBank Accession No.AA297444, related to a portion of SEQ ID NO: 1 is shown in SEQ ID NO:22.This public EST contains a region of 210 nucleotides that are related tonucleotides 1102-1311 of SEQ ID NO:1.

In another aspect, the invention provides an isolated nucleic acidmolecule comprising a polynucleotide which hybridizes under stringenthybridization conditions to a portion of the polynucleotide in a nucleicacid molecule of the invention described above, for instance, thefull-length cDNA set forth in SEQ ID NO:1 or the cDNA clone contained inATCC Deposit 97769. By “stringent hybridization conditions” is intendedovernight incubation at 42° C. in a solution comprising: 50% formamide,5×SSC (750 mM NaCl, 75 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 g/mldenatured, sheared salmon sperm DNA, followed by washing the filters in0.1×SSC at about 65° C.

By a polynucleotide which hybridizes to a “portion” of a polynucleotideis intended a polynucleotide (either DNA or RNA) hybridizing to at leastabout 15 nucleotides (nt), and more preferably at least about 20 nt,still more preferably at least about 30 nt, and even more preferablyabout 30-70 nt of the reference polynucleotide. These are useful asdiagnostic probes and primers as discussed above and in more detailbelow.

By a portion of a polynucleotide of “at least 20 nt in length,” forexample, is intended 20 or more contiguous nucleotides from thenucleotide sequence of the reference polynucleotide (e.g., the depositedcDNA or the nucleotide sequence as shown in SEQ ID NO:1).

Of course, a polynucleotide which hybridizes only to a poly A sequence(such as the 3¢ terminal poly(A) tract of the hCRY2 receptor cDNA shownin SEQ ID NO:1), or to a complementary stretch of T (or U) resides,would not be included in a polynucleotide of the invention used tohybridize to a portion of a nucleic acid of the invention, since such apolynucleotide would hybridize to any nucleic acid molecule containing apoly (A) stretch or the complement thereof (e.g., practically anydouble-stranded cDNA clone).

As indicated, nucleic acid molecules of the present invention whichencode a hCRY2 polypeptide may include, but are not limited to thoseencoding the amino acid sequence of the mature polypeptide, by itself;the coding sequence for the mature polypeptide and additional sequences,such as those encoding the about 22 amino acid leader or secretorysequence, such as a pre-, or pro- or prepro-protein sequence; the codingsequence of the mature polypeptide, with or without the aforementionedadditional coding sequences, together with additional, non-codingsequences, including for example, but not limited to introns andnon-coding 5¢ and 3¢ sequences, such as the transcribed, non-translatedsequences that play a role in transcription, mRNA processing, includingsplicing and polyadenylation signals, for example—ribosome binding andstability of mRNA; an additional coding sequence which codes foradditional amino acids, such as those which provide additionalfunctionalities. Thus, the sequence encoding the polypeptide may befused to a marker sequence, such as a sequence encoding a peptide whichfacilitates purification of the fused polypeptide. In certain preferredembodiments of this aspect of the invention, the marker amino acidsequence is a hexa-histidine peptide, such as the tag provided in a pQEvector (Qiagen, Inc.), among others, many of which are commerciallyavailable. As described in Gentz et al., Proc. Natl. Acad. Sci. USA86:821-824 (1989), for instance, hexa-histidine provides for convenientpurification of the fusion protein. The “HA” tag is another peptideuseful for purification which corresponds to an epitope derived from theinfluenza hemagglutinin protein, which has been described by Wilson etal., Cell 37: 767 (1984). As discussed below, other such fusion proteinsinclude the hCRY2 receptor fused to the maltose binding protein sequence(see Examples 1 and 2), or to Fc at the N- or C-terminus.

The present invention further relates to variants of the nucleic acidmolecules of the present invention, which encode portions, analogs orderivatives of the hCRY2 receptor. Variants may occur naturally, such asa natural allelic variant. By an “allelic variant” is intended one ofseveral alternate forms of a gene occupying a given locus on achromosome of an organism. Genes II, Lewin, B., ed., John Wiley & Sons,New York (1985). Non-naturally occurring variants may be produced usingart-known mutagenesis techniques.

Such variants include those produced by nucleotide substitutions,deletions or additions, which may involve one or more nucleotides. Thevariants may be altered in coding regions, non-coding regions, or both.Alterations in the coding regions may produce conservative ornon-conservative amino acid substitutions, deletions or additions.Especially preferred among these are silent substitutions, additions anddeletions, which do not alter the properties and activities of the hCRY2receptor or portions thereof. Also especially preferred in this regardare conservative substitutions.

Further embodiments of the invention include isolated nucleic acidmolecules comprising a polynucleotide having a nucleotide sequence atleast 95% identical, and more preferably at least 96%, 97%, 98% or 99%identical to (a) a nucleotide sequence encoding the polypeptide havingthe complete amino acid sequence in SEQ ID NO:2; (b) a nucleotidesequence encoding the polypeptide having the complete amino acidsequence in SEQ ID NO:2 except for the N-terminal methionine (amino acidresidues −21 to 571 in SEQ ID NO:2); (c) a nucleotide sequence encodingthe polypeptide having the amino acid sequence at positions from about 1to about 571 in SEQ ID NO:2; (d) a nucleotide sequence encoding thepolypeptide having the amino acid sequence at positions from about 191to about 571 in SEQ ID NO:2; (e) a nucleotide sequence encoding thehCRY2 polypeptide having the amino acid sequence encoded by the cDNAclone contained in ATCC Deposit No. 97769; (f) a nucleotide sequenceencoding the mature hCRY2 receptor having the amino acid sequenceencoded by the cDNA clone contained in ATCC Deposit No. 97769; (g) anucleotide sequence encoding the hCRY2 receptor extracellular domain;(h) a nucleotide sequence encoding the hCRY2 receptor transmembranedomain; (i) a nucleotide sequence encoding the hCRY2 receptorintracellular domain; (j) a nucleotide sequence encoding the hCRY2receptor extracellular and intracellular domains with all or part of thetransmembrane domain deleted; and (k) a nucleotide sequencecomplementary to any of the nucleotide sequences in (a), (b), (c), (d),(e), (f), (g), (h), (i), or (j).

By a polynucleotide having a nucleotide sequence at least, for example,95% “identical” to a reference nucleotide sequence encoding a hCRY2polypeptide is intended that the nucleotide sequence of thepolynucleotide is identical to the reference sequence except that thepolynucleotide sequence may include up to five point mutations per each100 nucleotides of the reference nucleotide sequence encoding the hCRY2receptor. In other words, to obtain a polynucleotide having a nucleotidesequence at least 95% identical to a reference nucleotide sequence, upto 5% of the nucleotides in the reference sequence may be deleted orsubstituted with another nucleotide, or a number of nucleotides up to 5%of the total nucleotides in the reference sequence may be inserted intothe reference sequence. These mutations of the reference sequence mayoccur at the 5¢ or 3¢ terminal positions of the reference nucleotidesequence or anywhere between those terminal positions, interspersedeither individually among nucleotides in the reference sequence or inone or more contiguous groups within the reference sequence.

As a practical matter, whether any particular nucleic acid molecule isat least 95%, 96%, 97%, 98% or 99% identical to, for instance, thenucleotide sequence shown in SEQ ID NO:1 or to the nucleotides sequenceof the deposited cDNA clone can be determined conventionally using knowncomputer programs such as the Bestfit program (Wisconsin SequenceAnalysis Package, Version 8 for Unix, Genetics Computer Group,University Research Park, 575 Science Drive, Madison, Wis. 53711.Bestfit uses the local homology algorithm of Smith and Waterman,Advances in Applied Mathematics 2: 482-489 (1981), to find the bestsegment of homology between two sequences. When using Bestfit or anyother sequence alignment program to determine whether a particularsequence is, for instance, 95% identical to a reference sequenceaccording to the present invention, the parameters are set, of course,such that the percentage of identity is calculated over the full lengthof the reference nucleotide sequence and that gaps in homology of up to5% of the total number of nucleotides in the reference sequence areallowed.

The present application is directed to nucleic acid molecules at least95%, 96%, 97%, 98% or 99% identical to the nucleic acid sequence shownin SEQ ID NO: 1 or to the nucleic acid sequence of the deposited cDNA,irrespective of whether they encode a polypeptide having hCRY2 receptoractivity. This is because even where a particular nucleic acid moleculedoes not encode a polypeptide having hCRY2 receptor activity, one ofskill in the art would still know how to use the nucleic acid molecule,for instance, as a hybridization probe or a polymerase chain reaction(PCR) primer. Uses of the nucleic acid molecules of the presentinvention that do not encode a polypeptide having hCRY2 receptoractivity include, inter alia, (1) isolating the hCRY2 receptor gene orallelic variants thereof in a cDNA library; (2) in situ hybridization(e.g., “FISH”) to metaphase chromosomal spreads to provide precisechromosomal location of the hCRY2 receptor gene, as described in Vermaet al., Human Chromosomes: A Manual of Basic Techniques, Pergamon Press,New York (1988); and (3) Northern Blot analysis for detecting hCRY2receptor mRNA expression in specific tissues.

Preferred, however, are nucleic acid molecules having sequences at least95%, 96%, 97%, 98% or 99% identical to the nucleic acid sequence shownin SEQ ID NO:1 or to the nucleic acid sequence of the deposited cDNAwhich do, in fact, encode a polypeptide having hCRY2 receptor activity.

Of course, due to the degeneracy of the genetic code, one of ordinaryskill in the art will immediately recognize that a large number of thenucleic acid molecules having a sequence at least 95%, 96%, 97%, 98%, or99% identical to the nucleic acid sequence of the deposited cDNA or thenucleic acid sequence shown in SEQ ID NO: 1 will encode a polypeptide“having hCRY2 receptor activity.” It will be further recognized in theart that, for such nucleic acid molecules that are not degeneratevariants, a reasonable number will also encode a polypeptide havinghCRY2 protein activity. This is because the skilled artisan is fullyaware of amino acid substitutions that are either less likely or notlikely to significantly effect protein function (e.g., replacing onealiphatic amino acid with a second aliphatic amino acid).

For example, guidance concerning how to make phenotypically silent aminoacid substitutions is provided in Bowie, J. U. et al., “Deciphering theMessage in Protein Sequences: Tolerance to Amino Acid Substitutions,”Science 247:1306-1310 (1990), wherein the authors indicate that proteinsare surprisingly tolerant of amino acid substitutions.

Vectors and Host Cells

The present invention also relates to vectors which include the isolatedDNA molecules of the present invention, host cells which are geneticallyengineered with the recombinant vectors, and the production of hCRY2polypeptides or fragments thereof by recombinant techniques.

The polynucleotides may be joined to a vector containing a selectablemarker for propagation in a host. Generally, a plasmid vector isintroduced in a precipitate, such as a calcium phosphate precipitate, orin a complex with a charged lipid. If the vector is a virus, it may bepackaged in vitro using an appropriate packaging cell line and thentransduced into host cells.

The DNA insert should be operatively linked to an appropriate promoter,such as the phage lambda PL promoter, the E. coli lac, trp and tacpromoters, the SV40 early and late promoters and promoters of retroviralLTRs, to name a few. Other suitable promoters will be known to theskilled artisan. The expression constructs will further contain sitesfor transcription initiation, termination and, in the transcribedregion, a ribosome binding site for translation. The coding portion ofthe mature transcripts expressed by the constructs will preferablyinclude a translation initiating at the beginning and a terminationcodon (UAA, UGA or UAG) appropriately positioned at the end of thepolypeptide to be translated.

As indicated, the expression vectors will preferably include at leastone selectable marker. Such markers include dihydrofolate reductase orneomycin resistance for eukaryotic cell culture and tetracycline orampicillin resistance genes for culturing in E. coli and other bacteria.Representative examples of appropriate heterologous hosts include, butare not limited to, bacterial cells, such as E. coli, Streptomyces andSalmonella typhimurium cells; fungal cells, such as yeast cells; insectcells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells suchas CHO, COS and Bowes melanoma cells; and plant cells. Appropriateculture mediums and conditions for the above-described host cells areknown in the art.

Among vectors preferred for use in bacteria include pQE70, pQE60 andpQE-9, available from Qiagen; pBS vectors, Phagescript vectors,Bluescript vectors, pNH8A, pNH16a, pNH18A, pNH46A, available fromStratagene; and ptrc99a, pKK223-3, pKK233-3, pDR540, pRIT5 availablefrom Pharmacia. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT,pOG44, pXT1 and pSG available from Stratagene; and pSVK3, pBPV, pMSG andpSVL available from Pharmacia. Other suitable vectors will be readilyapparent to the skilled artisan.

Introduction of the construct into the host cell can be effected bycalcium phosphate transfection, DEAE-dextran mediated transfection,cationic lipid-mediated transfection, electroporation, transduction,infection or other methods. Such methods are described in many standardlaboratory manuals, such as Davis et al., Basic Methods In MolecularBiology (1986).

The polypeptide may be expressed in a modified form, such as a fusionprotein, and may include not only secretion signals, but also additionalheterologous functional regions. For instance, a region of additionalamino acids, particularly charged amino acids, may be added to theN-terminus of the polypeptide to improve stability and persistence inthe host cell, during purification, or during subsequent handling andstorage. Also, peptide moieties may be added to the polypeptide tofacilitate purification. Such regions may be removed prior to finalpreparation of the polypeptide. The addition of peptide moieties topolypeptides to engender secretion or excretion, to improve stabilityand to facilitate purification, among others, are familiar and routinetechniques in the art. A preferred fusion protein comprises aheterologous region from immunoglobulin that is useful to solubilizeproteins. For example, EP-A-O 464 533 (Canadian counterpart 2045869)discloses fusion proteins comprising various portions of constant regionof immunoglobulin molecules together with another human protein or partthereof. In many cases, the Fc part in a fusion protein is thoroughlyadvantageous for use in therapy and diagnosis and thus results, forexample, in improved pharmacokinetic properties (EP-A 0232 262). On theother hand, for some uses it would be desirable to be able to delete theFe part after the fusion protein has been expressed, detected andpurified in the advantageous manner described. This is the case when Feportion proves to be a hindrance to use in therapy and diagnosis, forexample when the fusion protein is to be used as antigen forimmunizations. In drug discovery, for example, human proteins, such as,hIL5—has been fused with Fe portions for the purpose of high-throughputscreening assays to identify antagonists of hIL-5. See, D. Bennett etal., Journal of Molecular Recognition, Vol. 8:52-58 (1995) and K.Johanson et al., The Journal of Biological Chemistry, Vol. 270, No.16:9459-9471 (1995).

The hCRY2 receptor can be recovered and purified from recombinant cellcultures by well-known methods, including ammonium sulfate or ethanolprecipitation, acid extraction, anion or cation exchange chromatography,phosphocellulose chromatography, hydrophobic interaction chromatography,affinity chromatography, hydroxylapatite chromatography and lectinchromatography. Most preferably, high performance liquid chromatography(“HPLC”) is employed for purification. Polypeptides of the presentinvention include naturally purified products, products of chemicalsynthetic procedures, and products produced by recombinant techniquesfrom a prokaryotic or eukaryotic host, including, for example,bacterial, yeast, higher plant, insect and mammalian cells. Dependingupon the host employed in a recombinant production procedure, thepolypeptides of the present invention may be glycosylated or may benon-glycosylated. In addition, polypeptides of the invention may alsoinclude an initial modified methionine residue, in some cases as aresult of host-mediated processes.

hCRY2 Polypeptides and Fragments

The invention further provides an isolated hCRY2 polypeptide having theamino acid sequence encoded by the deposited cDNA, or the amino acidsequence in SEQ ID NO:2, or a peptide or polypeptide comprising aportion of the above polypeptides.

It will be recognized in the art that some amino acid sequences of thehCRY2 receptor can be varied without significant effect of the structureor function of the protein. If such differences in sequence arecontemplated, it should be remembered that there will be critical areason the protein which determine activity.

Thus, the invention further includes variations of the hCRY2 receptorwhich show substantial hCRY2 receptor activity or which include regionsof hCRY2 protein such as the protein portions discussed below. Suchmutants include deletions, insertions, inversions, repeats, and typesubstitutions. As indicated above, guidance concerning which amino acidchanges are likely to be phenotypically silent can be found in Bowie, J.U., et al., “Deciphering the Message in Protein Sequences: Tolerance toAmino Acid Substitutions,” Science 247:1306-1310 (1990).

Thus, the fragment, derivative or analog of the polypeptide of SEQ IDNO:2, or that encoded by the deposited cDNA, may be (i) one in which oneor more of the amino acid residues are substituted with a conserved ornon-conserved amino acid residue (preferably a conserved amino acidresidue) and such substituted amino acid residue may or may not be oneencoded by the genetic code, or (ii) one in which one or more of theamino acid residues includes a substituent group, or (iii) one in whichthe mature polypeptide is fused with another compound, such as acompound to increase the half-life of the polypeptide (for example,polyethylene glycol), or (iv) one in which the additional amino acidsare fused to the mature polypeptide, such as an IgG Fc fusion regionpeptide or leader or secretory sequence or a sequence which is employedfor purification of the mature polypeptide or a proprotein sequence.Such fragments, derivatives and analogs are deemed to be within thescope of those skilled in the art from the teachings herein.

Of particular interest are substitutions of charged amino acids withanother charged amino acid and with neutral or negatively charged aminoacids. The latter results in proteins with reduced positive charge toimprove the characteristics of the hCRY2 protein. The prevention ofaggregation is highly desirable. Aggregation of proteins not onlyresults in a loss of activity but can also be problematic when preparingpharmaceutical formulations, because they can be immunogenic (Pinckardet al., Clin. Exp. Immunol. 2:331-340 (1967); Robbins et al., Diabetes36:838-845 (1987); Cleland et al. Crit. Rev. Therapeutic Drug CarrierSystems 10:307-377 (1993)).

The replacement of amino acids can also change the selectivity ofbinding to cell surface receptors. Ostade et al. (Nature 361:266-268(1993)) describes certain mutations resulting in selective binding ofTNF-α to only one of the two known types of TNF receptors. Thus, thehCRY2 receptor of the present invention may include one or more aminoacid substitutions, deletions or additions, either from naturalmutations or human manipulation.

As indicated, changes are preferably of a minor nature, such asconservative amino acid substitutions that do not significantly affectthe folding or activity of the protein (see Table 1).

TABLE 1 Conservative Amino Acid Substitutions. Aromatic PhenylalanineTryptophan Tyrosine Hydrophobic Leucine Isoleucine Valine PolarGlutamine Asparagine Basic Arginine Lysine Histidine Acidic AsparticAcid Glutamic Acid Small Alanine Serine Threonine Methionine Glycine

Of course, the number of amino acid substitutions a skilled artisanwould make depends on many factors, including those described above.Generally speaking, the number of substitutions for any given hCRY2polypeptide will not be more than 50, 40, 30, 20, 10, 5, or 3.

Amino acids in the hCRY2 protein of the present invention that areessential for function can be identified by methods known in the art,such as site-directed mutagenesis or alanine-scanning mutagenesis(Cunningham and Wells, Science 244:1081-1085 (1989)). The latterprocedure introduces single alanine mutations at every residue in themolecule. The resulting mutant molecules are then tested for biologicalactivity such as receptor binding or in vitro, or in vitro proliferativeactivity. Sites that are critical for ligand-receptor binding can alsobe determined by structural analysis such as crystallization, nuclearmagnetic resonance or photoaffinity labeling (Smith et al., J. Mol.Biol. 224:899-904 (1992) and de Vos et al. Science 255:306-312 (1992)).

The polypeptides of the present invention are preferably provided in anisolated form. By “isolated polypeptide” is intended a polypeptideremoved from its native environment. Thus, a polypeptide produced orcontained in a recombinant host cell is considered “isolated” for thepurposes of the present invention. Also intended as “isolated” is apolypeptide that has been purified, partially or substantially, from arecombinant host or a native source. For example, a recombinantlyproduced version of the hCRY2 receptor can be substantially purified bythe one-step method described in Smith and Johnson, Gene 67:31-40(1988).

The polypeptides of the present invention also include the completepolypeptide encoded by the deposited cDNA; the mature polypeptideencoded by the deposited the cDNA; amino acid residues −22 to 571 of SEQID NO:2; amino acid residues −21 to 571 of SEQ ID NO:2; amino acidresidues 1 to 571 of SEQ ID NO:2; amino acid residues 191 to 571 of SEQID NO:2; the extracellular domain; the transmembrane domain; and theintracellular domain, as well as polypeptides which are at least 95%identical, more preferably at least 96%,97%, 98% or 99% identical to thepolypeptides described above, and also include portions of suchpolypeptides with at least 30 amino acids and more preferably at least50 amino acids.

By a polypeptide having an amino acid sequence at least, for example,95% “identical” to a reference amino acid sequence of a hCRY2polypeptide is intended that the amino acid sequence of the polypeptideis identical to the reference sequence except that the polypeptidesequence may include up to five amino acid alterations per each 100amino acids of the reference amino acid of the hCRY2 receptor. In otherwords, to obtain a polypeptide having an amino acid sequence at least95% identical to a reference amino acid sequence, up to 5% of the aminoacid residues in the reference sequence may be deleted or substitutedwith another amino acid, or a number of amino acids up to 5% of thetotal amino acid residues in the reference sequence may be inserted intothe reference sequence. These alterations of the reference sequence mayoccur at the amino or carboxy-terminal positions of the reference aminoacid sequence or anywhere between those terminal positions, interspersedeither individually among residues in the reference sequence or in oneor more contiguous groups within the reference sequence.

As a practical matter, whether any particular polypeptide is at least95%, 96%, 97%, 98% or 99% identical to those described above can bedetermined conventionally using known computer programs such as theBestfit program (Wisconsin Sequence Analysis Package, Version 8 forUnix, Genetics Computer Group, University Research Park, 575 ScienceDrive, Madison, Wis. 53711). When using Bestfit or any other sequencealignment program to determine whether a particular sequence is, forinstance, 95% identical to a reference sequence according to the presentinvention, the parameters are set, of course, such that the percentageof identity is calculated over the full length of the reference aminoacid sequence and that gaps in homology of up to 5% of the total numberof amino acid residues in the reference sequence are allowed.

The polypeptide of the present invention could be used as a molecularweight marker on SDS-PAGE gels or on molecular sieve gel filtrationcolumns using methods well known to those of skill in the art.

It is believed that the hCRY2 receptor is involved in the circadianregulation of mammalian physiology. Thus, ligands which bind to thehCRY2 receptor would be useful in treating patients with primary sleepdisorders (e.g., disorders with no apparent cause). Ligands which bindto the hCRY2 receptor would also be useful in treating patients withsleep disorders caused by odd working hours (e.g., among patients whowork during the night or who work rotating shifts).

It is also believed that the hCRY2 receptor is involved in mediatingrepair of damage to DNA, proteins, cells or tissue (e.g., skin) causedby ultraviolet light. Thus, ligands which bind to the hCRY2 receptorwould be useful in treating patients suffering from UV damage.

As indicated below, the hCRY2 polypeptides of the present invention canbe used to generate antibodies. Such antibodies can be used toinvestigate the expression, regulation, and ligand binding properties ofthe hCRY2 receptor.

In another aspect, the invention provides a peptide or polypeptidecomprising an epitope-bearing portion of a polypeptide of the invention.The epitope of this polypeptide portion is an immunogenic or antigenicepitope of a polypeptide described herein. An “immunogenic epitope” isdefined as a part of a protein that elicits an antibody response whenthe whole protein is the immunogen. On the other hand, a region of aprotein molecule to which an antibody can bind is defined as an“antigenic epitope.” The number of immunogenic epitopes of a proteingenerally is less than the number of antigenic epitopes. See, forinstance, Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).

As to the selection of peptides or polypeptides bearing an antigenicepitope (i.e., that contain a region of a protein molecule to which anantibody can bind), it is well known in that art that relatively shortsynthetic peptides that mimic part of a protein sequence are routinelycapable of eliciting an antiserum that reacts with the partiallymimicked protein. See, for instance, Sutcliffe, J. G., Shinnick, T. M.,Green, N. and Learner, R. A., Antibodies that react with predeterminedsites on protein, Science 219:660-666 (1983). Peptides capable ofeliciting protein-reactive sera are frequently represented in theprimary sequence of a protein, can be characterized by a set of simplechemical rules, and are confined neither to immunodominant regions ofintact proteins (i.e., immunogenic epitopes) nor to the amino orcarboxyl terminals.

Antigenic epitope-bearing peptides and polypeptides of the invention aretherefore useful to raise antibodies, including monoclonal antibodies,that bind specifically to a polypeptide of the invention. See, forinstance, Wilson et al., Cell 37:767-778 (1984) at 777.

Antigenic epitope-bearing peptides and polypeptides of the inventionpreferably contain a sequence of at least seven, more preferably atleast nine and most preferably between at least about 15 to about 30amino acids contained within the amino acid sequence of a polypeptide ofthe invention.

Non-limiting examples of antigenic polypeptides or peptides that can beused to generate hCRY2 receptor-specific antibodies include: apolypeptide comprising amino acid residues from about 8 to about 17 inSEQ ID NO:2; a polypeptide comprising amino acid residues from about 23to about 30 in SEQ ID NO:2; a polypeptide comprising amino acid residuesfrom about 55 to about 70 in SEQ ID NO:2; a polypeptide comprising aminoacid residues from about 74 to about 81 in SEQ ID NO:2; a polypeptidecomprising amino acid residues from about 136 to about 147 in SEQ IDNO:2; a polypeptide comprising amino acid residues from about 156 toabout 165 in SEQ ID NO:2; a polypeptide comprising amino acid residuesfrom about 231 to about 239 in SEQ ID NO:2; a polypeptide comprisingamino acid residues from about 271 to about 279 in SEQ ID NO:2; apolypeptide comprising amino acid residues from about 298 to about 309in SEQ ID NO:2; a polypeptide comprising amino acid residues from about316 to about 324 in SEQ ID NO:2; a polypeptide comprising amino acidresidues from about 328 to about 334 in SEQ ID NO:2; a polypeptidecomprising amino acid residues from about 415 to about 426 in SEQ IDNO:2; and a polypeptide comprising amino acid residues from about 512 toabout 519 in SEQ ID NO:2. As indicated above, the inventors havedetermined that the above polypeptide fragments are antigenic regions ofthe hCRY2 receptor protein.

The epitope-bearing peptides and polypeptides of the invention may beproduced by any conventional means. Houghten, R. A., General method forthe rapid solid-phase synthesis of large numbers of peptides:Specificity of antigen-antibody interaction at the level of individualamino acids, Proc. Natl. Acad. Sci. USA 82:5131-5135 (1985). This“Simultaneous Multiple Peptide Synthesis (SMPS)” process is furtherdescribed in U.S. Pat. No. 4,631,211 to Houghten et al. (1986).

As one of skill in the art will appreciate, hCRY2 polypeptides of thepresent invention and the epitope-bearing fragments thereof describedabove can be combined with parts of the constant domain ofimmunoglobulins (IgG), resulting in chimeric polypeptides. These fusionproteins facilitate purification and show an increased half-life invivo. This has been shown, e.g., for chimeric proteins consisting of thefirst two domains of the human CD4-polypeptide and various domains ofthe constant regions of the heavy or light chains of mammalianimmunoglobulins (EPA 394,827; Traunecker et al., Nature 331:84-86(1988)). Fusion proteins that have a disulfide-linked dimeric structuredue to the IgG part can also be more efficient in binding andneutralizing other molecules than the monomeric hCRY2 protein or proteinfragment alone (Fountoulakis et al., J. Biochem. 270:3958-3964 (1995)).

Detection of hCRY2 Gene Expression

The expression level of the hCRY2 gene can be readily assayed by one ofordinary skill in the art. By “assaying the expression level of the geneencoding the hCRY2 protein” is intended qualitatively or quantitativelymeasuring or estimating the level of the hCRY2 protein or the level ofthe mRNA encoding the hCRY2 receptor in a biological sample (e.g., bydetermining or estimating absolute protein level or mRNA level).

By “biological sample” is intended any biological sample obtained froman individual, cell line, tissue culture, or other source which containshCRY2 protein or mRNA. Such tissues include cerebellum, retina, breast,pituitary, heart, placenta, lung, skeletal muscle, kidney, and pancreas.Biological samples include mammalian tissues which contain hCRY2protein. Preferred mammals include monkeys, apes, cats, dogs, cows,pigs, horses, rabbits, and humans. Particularly preferred are humans.

Total cellular RNA can be isolated from a biological sample using thesingle-step guanidinium-thiocyanate-phenol-chloroform method describedin Chomezynski and Sacchi (Anal. Biochem. 162:156-159 (1987)). Levels ofmRNA encoding the hCRY2 receptor are then assayed using any appropriatemethod. These include Northern blot analysis (Harada et al., Cell63:303-312 (1990)), S1 nuclease mapping (Harada et al., Cell 63:303-312(1990)), the polymerase chain reaction (PCR), reverse transcription incombination with the polymerase chain reaction (RT-PCR) (Fujita et al.,Cell 49:35-36 (1990)), and reverse transcription in combination with theligase chain reaction (RT-LCR).

As discussed supra, assaying hCRY2 protein levels in a biological samplecan occur using antibody-based techniques. For example, hCRY2 proteinexpression in tissues can be studied with classical immunohistologicalmethods (Jalkanen, M. et al., J. Cell. Biol. 101:976-985 (1985);Jalkanen, M. et al., J. Cell. Biol. 105: 3087-3096 (1987)). Otherantibody-based methods useful for detecting hCRY2 receptor geneexpression include immunoassays, such as the enzyme linked immunosorbentassay (ELISA) and the radioimmunoassay (RIA). Suitable labels are knownin the art and include enzyme labels, such as glucose oxidase, andradioisotopes, such as iodine (¹²⁵I, ¹²¹I), carbon (¹⁴C), sulfur (³⁵S),tritium (³H), indium (¹¹²In), and technetium (^(99m)Tc), and fluorescentlabels, such as fluorescein and rhodamine, and biotin.

Chromosome Assays

The nucleic acid molecules of the present invention are also valuablefor chromosome identification. The sequence is specifically targeted toand can hybridize with a particular location on an individual humanchromosome. The mapping of DNAs to chromosomes according to the presentinvention is an important first step in correlating those sequences withgenes associated with disease.

In certain preferred embodiments in this regard, the cDNA hereindisclosed is used to clone genomic DNA of a hCRY2 receptor gene. Thiscan be accomplished using a variety of well known techniques andlibraries, which generally are available commercially. The genomic DNAthen is used for in situ chromosome mapping using well known techniquesfor this purpose.

In addition, in some cases, sequences can be mapped to chromosomes bypreparing PCR primers (preferably 15-25 bp) from the cDNA. Computeranalysis of the 3¢ untranslated region of the gene is used to rapidlyselect primers that do not span more than one exon in the genomic DNA,thus complicating the amplification process. These primers are then usedfor PCR screening of somatic cell hybrids containing individual humanchromosomes.

Fluorescence in situ hybridization (“FISH”) of a cDNA clone to ametaphase chromosomal spread can be used to provide a precisechromosomal location in one step. This technique can be used with probesfrom the cDNA as short as 50 or 60 bp. For a review of this technique,see Verma et al., Human Chromosomes: A Manual Of Basic Techniques,Pergamon Press, New York (1988).

Once a sequence has been mapped to a precise chromosomal location, thephysical position of the sequence on the chromosome can be correlatedwith genetic map data. Such data are found, for example, in V. McKusick,Mendelian Inheritance In Man, available on-line through Johns HopkinsUniversity, Welch Medical Library. The relationship between genes anddiseases that have been mapped to the same chromosomal region are thenidentified through linkage analysis (coinheritance of physicallyadjacent genes).

Next, it is necessary to determine the differences in the cDNA orgenomic sequence between affected and unaffected individuals. If amutation is observed in some or all of the affected individuals but notin any normal individuals, then the mutation is likely to be thecausative agent of the disease.

Having generally described the invention, the same will be more readilyunderstood by reference to the following examples, which are provided byway of illustration and are not intended as limiting.

EXAMPLE 1 Cloning the Human Photoreceptor

The cDNA clone (R1931) for the human photolyase homolog (Adams, M. D. etal., Nature 377:3-174 (1995)), carrying the 3′ terminal 1038 bp of theopen reading frame gene, was obtained from R. K. Wilson (WashingtonUniversity, St. Louis). The 5′ terminal part of the gene was obtainedusing the 5′ RACE System for Rapid Amplification of cDNA ends (GibcoBRL,Gaithersburg, Md., USA) as described by the manufacturer and using mRNAfrom the T093 human fibroblast cell line. The amplified product wasdigested with NcoI and Hind III and cloned into the Nco I/Hind III sitesof the baculovirus expression vector p2Bac (Invitrogen, San Diego,Calif., USA) and the E. coli expression vector pKK233-2 (Pharmacia,Uppsala, Sweden). Sequence of the gene was confirmed by double strandDNA sequencing using the Sequenase DNA sequencing kit (US Biochemical,Arlington, Ill., USA) and was in complete agreement with the previouslypublished sequence (Todo, T. et al., Science 272:109-112 (1996)). Amaltose binding protein (MBP) fusion construct was made by inserting theBgl II/Hind III fragment carrying the entire photolyase homolog codingregion into the H I/Hind III site of the MBP expression vector pMal-c2(NEB, Beverly, Mass., USA). This construct was named pDH1996-1.

The sequence of the second homolog was first identified by searching adatabase containing approximately 1 million human ESTs, which wasgenerated using high throughput automated DNA sequence analysis ofrandomly selected human cDNA clones (Adams, M. D. et al., Nature377:3-174 (1995); Adams, M. D. et al., Nature 355:632-634 (1992); andAdams, M. D. et al., Science 252:1651-1656 (1991)). Sequence homologycomparisons of each EST were performed against the GenBank databaseusing the blastn and tblastn algorithms (Altschul, S. F. et al., J. Mol.Biol. 215:403-410 (1990)). A specific homology search using the knownhuman photolyase homolog 1 amino acid sequence against this human ESTdatabase revealed two ESTs (HGS6392 and HGS47815). Both were from ahuman fetal brain cDNA library, with greater than 84% homology to thefirst homolog. The two ESTs are identical except HGS47815 is 183 bplonger at the 5′ end. HGS47815 contains 3035 bp and the sequencecomparison suggested that it is missing approximately 1 kb of theputative photolyase homolog at the 5′ end. Using this clone as a probe,a hybridization screening was conducted through the human fetal braincDNA library from which HGS6392 and HGS47815 were initially discovered.From this screening, a positive clone (SO5), which was 466 bp longerthan HGS47815, was identified.

The gene identified previously (Adams et al. (1995); Todo et al. (1996)has been designated hCRY1. In the present specification, the humanphotolyase homolog genes are referred to as hCRY1 and hCRY2 and thecorresponding gene products are referred to at hCRY1 and hCRY2,respectively. These names are in compliance with the nomenclature forblue-light photoreceptors (i.e., cryptochromes) in plants (Short, T. W.et al., Ann. Rev. Plant. Physiol. Plant Mol. Biol. 45:143-171 (1994)).The gene of the present invention has been designated hCRY2.

The hCRY2 gene was originally identified in a human fetal brain cDNAlibrary and was found to be expressed in fibroblasts as well. Further,the hCRY2 gene was detected in human cDNA libraries prepared from fetalbrain, synovial sarcoma, resting T-cell, infant brain, cerebellum,endometrial tumor, testes tumor, adult retina, chondrosarcoma, breast,and pituitary. Compared to hCRY1, hCRY2 occurred at lower frequency inthe human cDNA database in all tissues tested.

To obtain the entire 5′ terminal part of the hCRY2 gene, the RACE PCRprocedure was used. Briefly, a specific primer for the 3 end of thegene, 5′-GGGCTCTGCCACAGGGTGACTGAGGTC-3′ (SEQ ID NO:7), was used forfirst strand cDNA synthesis. First round of PCR amplification for the 5′terminal part of the hCRY2 gene was carried out using a gene specificprimer, 5′-AATACCCGGACCCCGCTC-3′ (SEQ ID NO:8), at the 3′ end of thegene and a degenerative primer at the 5′ end as described by themanufacturer. This was followed by a second round of amplification usinganother gene specific primer, 5′CAGGTCCCACAGGCGGTA-3′ (SEQ ID NO:9) atthe 3′ end of the gene and another degenerative primer at the 5′ end.Sequence comparison of the open reading frame of the amplified productto the first photolyase homolog confirmed that the 5 end of the gene hadbeen cloned.

A MBP fusion of the S05 clone was constructed by ligating anEcoRI/BglIII fragment containing the entire open reading frame of S05into the EcoRI/HI site of pMal-c2. This construct, which encodes thecarboxy terminal 381 amino acids of the hCRY2 protein (amino acidresidues 191-571 in SEQ ID NO:2), was named pDH1996-2.

Large scale sequencing of expression sequence tagged (EST) cDNAsrevealed a clone with homology to the microbial photolyase genes. Thisclone was designated a photolyase isolog since there is no convincingevidence that humans have a photolyase which can repair cyclobutanepyrimidine dimers (Adams, M. D. et al., Nature 377:3-174 (1995)).Independently, Todo et al. cloned and sequenced the gene for theapoenzyme of the newly discovered (6-4) photolyase from D. melanogaster(Todo, T. et al., Science 272:109-112 (1996)). It was found that the(6-4) photolyase has high degree of homology with thephotolyase/blue-light photoreceptor family of proteins (Ahmad, M. etal., Nature 366:162-166 (1993); Malhotra,K. et al., Biochemistry34:6892-6899 (1995)), including the human photolyase isolog. In fact,when the entire cDNA of the human photolyase isolog was isolated andsequenced, it revealed an astonishing 48% sequence identity with the D.melanogaster (6-4) photolyase (Todo, T. et al., Science 272:109-112(1996)).

Sequence comparison of the hCRY1 and hCRY2 proteins, along with arepresentative member of a type I (microbial) class photolyase, theblue-light photoreceptor gene HY4 of A. thaliana, and the (6-4)photolyase of D. melanogaster, are shown in FIGS. 4A-4C. hCRY1 and hCRY2exhibit 65% sequence identity at the nucleotide level and 74% sequenceidentity at the amino acid level. hCRY2 also shows high degree ofsequence homology to D. melanogaster (6-4) photolyase with a 51%sequence identity over the entire length.

Aside from the high degree of sequence homology between hCRY1 and hCRY2,the most noteworthy feature of the sequences of these proteins is thecomplete divergence over the carboxy-terminal 80 amino acids. A similardivergence has been found between the two A. thaliana blue-lightphotoreceptors (Ahmad, M. et al., Plant Molec. Biol. 30:851-861 (1996)).It is believed that this “tail” region of the A. thaliana photoreceptorinteracts with an effector molecule (Lin, C. et al., Proc. Natl. Acad.Sci. USA 98:6389-6393 (1995)). It is also believed that the hCRY1 andhCRY2 proteins also interact with downstream targets.

EXAMPLE 2 Purification of Recombinant human CRY Proteins

hCRY1 and hCRY2 proteins were expressed as MBP fusion proteins, usingthe MBP fusion vector pMal-c2 (FIG. 5), in DR153 E. coli cells. ThehCRY1 construct was called pDH1996-1. The hCRY2 construct was calledpDH1996-2. As discussed supra, pDH1996-2 contains the carboxy terminal381 amino acids (amino acid residues 191-571 in SEQ ID NO:2).Oligonucleotide primers were used to amplify the hCRY2 sequence. The 5′primer sequence was 5′-CGCGAATTCCTCCCTGGAGGAGCTGGG-3′ (SEQ ID NO:10),which contains the underlined EcoR I restriction site followed by 19bases corresponding to nucleotides 635-654 in the sequence set forth inSEQ ID NO:1. The 3′ primer sequence was5′-GCGAGATCTTCAGGCATCCTTGCTCGG-3′ (SEQ ID NO:11), which contains theunderlined Bgl II restriction site, followed by 18 bases reverse andcomplementary to nucleotides 1825-1842 in the sequence set forth in SEQID NO:1.

A longer MBP-hCRY2 fusion protein, containing amino acid residues −15 to571 of the sequence set forth in SEQ ID NO:2, was expressed in DR153cells using the pMal-c2 vector. Oligonucleotide primers were used toamplify the longer hCRY2 sequence. The 5′ primer sequence was5′-GCGGATATCG-CGGCAGCTGTGGCCCCG-3′ (SEQ ID NO: 12), which contains theunderlined EcoR V restriction site followed by 18 bases corresponding tonucleotides 22-39 in the sequence set forth in SEQ ID NO: 1. The 3′primer sequence was 5′-GCGAAGCTTTCAGGCATCCTTGCTCGG-3′ (SEQ ID NO:13),which contains the underlined Hind III restriction site, followed by 18bases reverse and complementary to nucleotides 1825-1842 in the sequenceset forth in SEQ ID NO:1. This amplified fragment was digested with EcoRV and Hind III prior to ligation into the pMal-c2 vector (afterdigestion of the vector with Xmn I and Hind III).

Expressed proteins were purified by affinity chromatography on amyloseresin (Malhotra, K. et al., Biochemistry 34:6892-6899 (1995)). Since thepossibility exists that fusion with MBP may interfere with enzymaticfunction, a MBP fusion form of the D. melanogaster (6-4) photolyase(Todo, T. et al., Science 272: 109-112 (1996)) was used as a control. Asdiscussed supra, the (6-4) photolyase is highly homologous to the hCRY1and hCRY2 photoreceptors and was prepared and purified as were the hCRY1and hCRY2 proteins.

EXAMPLE 3 Spectroscopic Properties of hCRY1 and hCRY2

All photolyases and blue-light photoreceptors that have beencharacterized to date contain FAD and a second chromophore, which is afolate in most organisms. In a few species which can synthesizedeazaflavin, the second photolyase chromophore is deazariboflavin (Eker,A. P. et al., J. Biol. Chem. 265:8009-8015 (1990); Malhotra, K. et al.,Biochemistry 34: 6892-6899 (1995)). hCRY1 and hCRY2 were assayed for thepresence of chromophores. The absorption spectra of the purified hCRY1and hCRY2 proteins were recorded with a Hewlett-Packard Model 8451Aspectrophotometer and the fluorescence spectra of the chromophores weremeasured at 22° C. in a Shimadzu RF5000 U Spectrofluorometer.

The absorption spectra of the MBP fusion forms of hCRY 1 and hCRY2(amino acids residues 191-571 in SEQ ID NO:2) are shown in FIG. 6A. Bothproteins exhibited a distinct 420 nm peak with residual absorptionextending all the way to 700 nm. The absorption spectra were almostidentical to the absorption spectra of the cyclobutane pyrimidine dimerphotolyase (Kim, S. T. et al., Mutation Res. 363:97-104 (1996)) and the(6-4) photolyase (data not shown) from D. melanogaster.

It has been demonstrated that the D. melanogaster T<>T photolyasecontained FAD and folate as chromophores (Kim, S. T. et al., MutationRes. 363:97-104 (1996)). Hence, it was reasoned that hCRY1 and hCRY2 mayalso contain these cofactors. A simple assay revealed that this isindeed the case. hCRY1 and hCRY2 were denatured by heating for 10minutes at 65° C. in 0.1 M HCL and 0.8% SDS. Following centrifugation toremove the protein precipitate, excitation and emission fluorescencespectra were recorded. FIG. 6B shows a diagnostic flavin fluorescencespectrum. It was concluded that both hCRY1 and hCRY2 contain flavin.Furthermore, upon increasing the pH to 10 by addition of NaOH, theflavin fluorescence was severely quenched, further confirming thecofactor as FAD (Faeder, E. J., Anal. Biochem. 53:332-336 (1973)).

Alkaline pH had another notable effect on the fluorescence spectrum: anew species with an excitation maximum at 380 and emission maximum at470 appeared (FIG. 6C). This behavior is typical of reduced pterin,which is non-fluorescent but is converted to highly fluorescent oxidizedpterin upon incubation in alkaline solutions (Johnson, J. L. et al.,Proc. Natl. Acad. Sci. USA 85:2046-2050 (1988)). Furthermore, theexcitation and emission spectra of the second chromophore are identicalto that of the D. melanogaster T<>T photolyase, which was shown to be afolate by TLC analysis with appropriate standards (Kim, S. T. et al.,Mutation Res. 363:97-104 (1996)). Thus, it was concluded that hCRY1 andhCRY2, like other members of the photolyase/photoreceptor family,contain FAD and a pterin as the two chromophore/cofactors.

EXAMPLE 4 Photolyase Activity Assay

In a photolyase assay, the restoration of the susceptibility to cleavageof the TTAA sequence by the MseI restriction endonuclease was measuredin a DNA fragment where the TT is either in the form of a cyclobutanethymine dimer (T<>T) or (6-4) photoproduct (Malhotra, K. et al.,Biochemistry 34:6892-6899 (1995); Kim, S. T. et al., Photochem.Photobiol. 63:292-295 (1996)). A 54 mer oligonucleotide duplex, and a49mer oligonucleotide duplex, containing a centrally located T<>T andT[6-4]T, respectively, were prepared as described previously (Smith, C.A., J. Biol. Chem. 268:11143-11151 (1993)) and were kindly provided byDr. J. S. Taylor (Washington University).

In the photoreactivation assay, hCRY1 and hCRY 2 (amino acids residues191-571 in SEQ ID NO:2) proteins (40 nM) were mixed with 0.5 nMsubstrate in a 50 μl reaction containing 50 mM Tris pH 7.4, 100 mM NaCl,6 mM dithiothreitol, 2 mM EDTA, 5 μg bovine serum albumin and 5%glycerol. The mixture was incubated in the dark at room temperature for10 minutes and then exposed to photoreactivating light (λ_(max)=366 nm),at 4° C. for 1 hour, from a Sylvania black light (Model B-100) at afluence rate of 2 milliwatts/cm2. The DNA was then extracted withphenol/chloroform, precipitated with ethanol, resuspended in restrictionenzyme buffer and digested with 8 units of MseI for 1 hour. The reactionproducts were electrophoresed on a 8% denaturing gel and the level ofdigested (repaired) DNA was determined by a Phospholmager (MolecularDynamics Inc.). For the (6-4) photoproduct, the level of 21mer detectedindicated the extent of repair. For the T<>T substrate, the level of19mer detected indicated the extent of repair.

The spectroscopic properties of hCRY1 and hCRY2 (supra) were consistentwith these proteins being a Pyr<>Pyr photolyase, a (6-4) photolyase, ora photoreceptor. To differentiate between these possibilities, therecombinant proteins were tested for repair activity. E. coli photolyaserepaired a T<>T photoproduct. 54% of the T<>T substrate was repaired.However, both CRY1 and hCRY2 failed to repair the T<>T photoproduct.

D. melanogaster (6-4) photolyase repaired a T[6-4]T photoproduct. 48% ofthe photoproduct was repaired. In contrast, both CRY1 and hCRY2 failedto repair the T[6-4]T photoproduct. After conducting the repairexperiments were under a variety of conditions (higher proteinconcentration and higher dose of photoreactivating light), it wasconcluded that hCRY1 and hCRY2 cannot have more than 0.1% of thephotolyase activities detected with bona fide photolyases. Thus, it wasconcluded that the recombinant photolyase homologs do not havephotolyase activity.

Even though these data strongly suggest that hCRY1 and hCRY2 are notphotolyases, it is conceivable that the proteins expressed inheterologous system were somewhat misfolded or lacked aposttranslational modification necessary for activity. Hence, thenatural sources were tested for activity. Cell-free extracts fromfibroblasts (T093), which expressed hCRY1 and hCRY2 (as revealed byprimer extension (for both hCRY1 and hCRY2) and immunoblotting (forhCRY1 only), failed to show any (6-4) photolyase activity.

To ascertain whether this lack of activity was due to inhibition byother proteins known to exist in cell-free extracts which bind to (6-4)photoproduct (Chu, G. et al., Science 242:564-567 (1988); Ghosh, R. etal., Proc. Natl. Acad. Sci. USA 93:6918-6923 (1996); Wakasugi, M. etal., Nucl. Acids Res. 24:1099-1104 (1996)), Drosophila (6-4) photolyasewas mixed with the fibroblast cell free extract and this mixture wasassayed for photoreactivation activity using a T(6-4)T substrate. Assayswith human cell free extract (infra) were performed in a similar manneras describe supra, except that 50 μg of CFE was used in the reaction.

In the absence of cell-free extract, Drosophila (6-4) photolyaserepaired 38% of the T(6-4) substrate. In the presence of cell-freeextract, Drosophila (6-4) photolyase repaired 29% of the substrate. Thislevel of inhibition cannot explain the total lack of photolyase activityin the cell-free extract, which was assayed under a variety ofconditions.

Finally, hCRY1 purified from a baculovirus/insect cell expression systemalso failed to show any photolyase activity (data not shown). Thus,hCRY1 and hCRY2 do not appear to possess a photolyase activity.

The longer form of the MBP-hCRY2 fusion protein, containing amino acids−15 to 571 in SEQ ID NO:2, displayed spectral properties similar tothose of the MBP-hCRY2 fusion protein that contained only amino acidresidues 191-571. Like the shorter MBP-hCRY2 fusion protein, the longerMBP-hCRY2 fusion protein failed to exhibit photolyase activity.

Many attempts from several labs to detect and isolate photolyases fromhuman cells have failed, leading to a near-consensus in the field thathumans do not have photolyase (Ley, R. D., Proc. Natl. Acad. Sci. USA98:4337 (1993); Li, Y. F. et al., Proc. Natl. Acad. Sci. USA90:4389-4393 (1993); Kato, T. et al., Nucl. Acids. Res. 22:4119-4124(1994)). However, the recent discovery of a photolyase for (6-4)photoproducts, and the finding that it belongs in thephotolyase/photoreceptor family of proteins (Todo, T. et al., Nature361:371-374 (1996)), raised the interesting possibility that humansmight have a (6-4) photolyase. Furthermore, a human homolog, with 48%sequence identity with D. melanogaster (6-4) photolyase, was identified(Todo et al., (1996)). The encoded protein could have been the elusivecyclobutane pyrimidine dimer photolyase described by Sutherland et al.,(Proc. Natl. Acad. Sci. USA 92:9732-9736 (1996)), a (6-4) photolyasewhich had not been searched for in humans in a systematic way, or aphotoreceptor. This present work was undertaken to differentiate betweenthese possibilities.

The results of the present work clearly show that the human (6-4)photolyase homolog identified previously (hCRY1) and the new homologidentified herein (hCRY2) are neither (6-4) photolyase nor cyclobutanepyrimidine dimer photolyase. Work with recombinant proteins and humancell free extract showed that the proteins encoded by these two genesneither bind to UV damaged DNA (data not shown) nor repair T<>T orT[6-4]T photoproducts in the absence or presence of light. Thus, one isleft with the third alternative, that the proteins encoded by the hCRY1and hCRY2 genes function as blue-light photoreceptors.

EXAMPLE 5 Cloning and Expression of hCRY2 Protein in a BaculovirusExpression System

In this illustrative example, the plasmid shuttle vector pA2 is used toinsert the cloned DNA encoding the complete protein, including itsnaturally associated secretary signal (leader) sequence, into abaculovirus to express the mature hCRY2 protein, using standard methodsas described in Summers et al., A Manual of Methods for BaculovirusVectors and Insect Cell Culture Procedures, Texas AgriculturalExperimental Station Bulletin No. 1555 (1987). This expression vectorcontains the strong polyhedrin promoter of the Autographa californicanuclear polyhedrosis virus (AcMNPV) followed by convenient restrictionsites such as BamH I and Asp 718. The polyadenylation site of the simianvirus 40 (“SV40”) is used for efficient polyadenylation. For easyselection of recombinant virus, the plasmid contains thebeta-galactosidase gene from E. coli under control of a weak promoter inthe same orientation, followed by the polyadenylation signal of thepolyhedrin gene. The inserted genes are flanked on both sides by viralsequences for cell-mediated homologous recombination with wild-typeviral DNA to generate viable virus that express the clonedpolynucleotide.

Many other baculovirus vectors could be used in place of the vectorabove, such as pAc373, pVL941 and pAcIM1, as one skilled in the artwould readily appreciate, as long as the construct providesappropriately located signals for transcription, translation, secretionand the like, including a signal peptide and an in-frame AUG asrequired. Such vectors are described, for instance, in Luckow et al.,Virology 170:31-39.

The cDNA sequence encoding the full length hCRY2 protein in thedeposited clone, including the AUG initiation codon and the naturallyassociated leader sequence shown in SEQ ID NO:2, is amplified using PCRoligonucleotide primers corresponding to the 5′ and 3′ sequences of thegene. The 5′ primer has the sequence5′-GCGAGATCTCCGCCATCATGGCGGCAACTGTGGCAAC-3′ (SEQ ID NO: 14) containingthe underlined Bgl II restriction enzyme site, an efficient signal forinitiation of translation in eukaryotic cells, as described by Kozak,M., J. Mol. Biol. 196:947-950 (1987), followed by 20 bases of thesequence of the complete hCRY2 protein shown in SEQ ID NO:1, beginningwith the AUG initiation codon. The 3′ primer has the sequence5′-GCGTCTAGATCAGGCATCCTTGCTCGG-3′ (SEQ ID NO: 15) containing theunderlined Xba I restriction site, followed by 18 nucleotides reverseand complementary to nucleotides 1825-1842 in SEQ ID NO:1

The amplified fragment is isolated from a 1% agarose gel using acommercially available kit (“Geneclean,” BIO 101 Inc., La Jolla,Calif.). The fragment then is digested with Bgl II and Xba I and againis purified on a 1% agarose gel. This fragment is designated herein“F1”.

The pA2 vector is digested with the restriction enzymes BamH I and Xba Iand optionally, can be dephosphorylated using calf intestinalphosphatase, using routine procedures known in the art. The DNA is thenisolated from a 1% agarose gel using a commercially available kit(“Geneclean” BIO 101 Inc., La Jolla, Calif.). This vector DNA isdesignated herein “V1”.

Fragment F1 and the dephosphorylated plasmid VI are ligated togetherwith T4 DNA ligase. E. coli HB101 or other suitable E. coli hosts suchas XL-1 Blue (Stratagene Cloning Systems, La Jolla, Calif.) cells aretransformed with the ligation mixture and spread on culture plates.Bacteria are identified that contain the plasmid with the human hCRY2gene using the PCR method, in which one of the primers that is used toamplify the gene and the second primer is from well within the vector sothat only those bacterial colonies containing hCRY2 gene fragment willshow amplification of the DNA. The sequence of the cloned fragment isconfirmed by DNA sequencing. This plasmid is designated hereinpBachCRY2.

Five μg of the plasmid pBachCRY2 is co-transfected with 1.0 μg of acommercially available linearized baculovirus DNA (“BaculoGold™baculovirus DNA”, Pharmingen, San Diego, Calif.), using the lipofectionmethod described by Felgner et al., Proc. Natl. Acad. Sci. USA84:7413-7417 (1987). 1 μg of BaculoGold™ virus DNA and 5 μg of theplasmid pBachCRY2 are mixed in a sterile well of a microtiter platecontaining 50 μl of serum-free Grace's medium (Life Technologies Inc.,Gaithersburg, Md.). Afterwards, 10 μl Lipofectin plus 90 μl Grace'smedium are added, mixed and incubated for 15 minutes at roomtemperature. Then the transfection mixture is added drop-wise to Sf9insect cells (ATCC CRL 1711) seeded in a 35 mm tissue culture plate with1 ml Grace's medium without serum. The plate is rocked back and forth tomix the newly added solution. The plate is then incubated for 5 hours at27° C. After 5 hours, the transfection solution is removed from theplate and 1 ml of Grace's insect medium supplemented with 10% fetal calfserum is added. The plate is put back into an incubator and cultivationis continued at 27° C. for four days.

After four days, the supernatant is collected and a plaque assay isperformed, as described by Summers and Smith, supra. An agarose gel with“Blue Gal” (Life Technologies Inc., Gaithersburg) is used to allow easyidentification and isolation of gal-expressing clones, which produceblue-stained plaques. (A detailed description of a “plaque assay” ofthis type can also be found in the user's guide for insect cell cultureand baculovirology distributed by Life Technologies Inc., Gaithersburg,page 9-10). After appropriate incubation, blue stained plaques arepicked with the tip of a micropipettor (e.g., Eppendorf). The agarcontaining the recombinant viruses is then resuspended in amicrocentrifuge tube containing 200 μl of Grace's medium and thesuspension containing the recombinant baculovirus is used to infect Sf9cells seeded in 35 mm dishes. Four days later, the supernatants of theseculture dishes are harvested and then they are stored at 4° C. Therecombinant virus is called V-hCRY2.

To verify the expression of the hCRY2 gene, Sf9 cells are grown inGrace's medium supplemented with 10% heat inactivated FBS. The cells areinfected with the recombinant baculovirus V-hCRY2 at a multiplicity ofinfection (“MOI”) of about 2. Six hours later the medium is removed andis replaced with SF900 II medium minus methionine and cysteine(available from Life Technologies Inc., Rockville, Md.). If radiolabeledproteins are desired, 42 hours later, 5 μCi of ³⁵S-methionine and 5 μCi³⁵S-cysteine (available from Amersham) are added. The cells are furtherincubated for 16 hours and then they are harvested by centrifugation.The proteins in the supernatant as well as the intracellular proteinsare analyzed by SDS-PAGE followed by autoradiography (if radiolabeled).Microsequencing of the amino acid sequence of the amino terminus ofpurified protein may be used to determine the amino terminal sequence ofthe mature protein and thus the cleavage point and length of thesecretory signal peptide.

EXAMPLE 6 Cloning and Expression of hCRY2 in Mammalian Cells

A typical mammalian expression vector contains the promoter element,which mediates the initiation of transcription of mRNA, the proteincoding sequence, and signals required for the termination oftranscription and polyadenylation of the transcript. Additional elementsinclude enhancers, Kozak sequences and intervening sequences flanked bydonor and acceptor sites for RNA splicing. Highly efficienttranscription can be achieved with the early and late promoters fromSV40, the long terminal repeats (LTRS) from Retroviruses, e.g., RSV,HTLVI, HIVI and the early promoter of the cytomegalovirus (CMV).However, cellular elements can also be used (e.g., the human actinpromoter). Suitable expression vectors for use in practicing the presentinvention include, for example, vectors such as PSVL and PMSG(Pharmacia, Uppsala, Sweden), pRSVcat (ATCC 37152), pSV2dhfr (ATCC37146) and pBC12MI (ATCC 67109). Mammalian host cells that could be usedinclude, human Hela 293, H9 and Jurkat cells, mouse NIH3T3 and C127cells, Cos 1, Cos 7 and CV 1, quail QC1-3 cells, mouse L cells andChinese hamster ovary (CHO) cells.

Alternatively, the gene can be expressed in stable cell lines thatcontain the gene integrated into a chromosome. The co-transfection witha selectable marker such as dhfr, gpt, neomycin, or hygromycin allowsthe identification and isolation of the transfected cells.

The transfected gene can also be amplified to express large amounts ofthe encoded protein. The DHFR (dihydrofolate reductase) marker is usefulto develop cell lines that carry several hundred or even severalthousand copies of the gene of interest. Another useful selection markeris the enzyme glutamine synthase (GS) (Murphy et al., Biochem. J.227:277-279 (1991); Bebbington et al., Bio/Technology 10: 169-175(1992)). Using these markers, the mammalian cells are grown in selectivemedium and the cells with the highest resistance are selected. Thesecell lines contain the amplified gene(s) integrated into a chromosome.Chinese hamster ovary (CHO) and NSO cells are often used for theproduction of proteins.

The expression vectors pC1 and pC4 contain the strong promoter (LTR) ofthe Rous Sarcoma Virus (Cullen et al., Molecular and Cellular Biology,438447 (March, 1985)) plus a fragment of the CMV-enhancer (Boshart etal., Cell 41:521-530 (1985)). Multiple cloning sites, e.g., with therestriction enzyme cleavage sites BamHI, XbaI and Asp718, facilitate thecloning of the gene of interest. The vectors contain in addition the 3′intron, the polyadenylation and termination signal of the ratpreproinsulin gene.

EXAMPLE 6(a) Cloning and Expression in COS Cells

The expression plasmid, phCRY2 HA, is made by cloning a cDNA encodinghCRY2 into the expression vector pcDNAI/Amp or pcDNAIII (which can beobtained from Invitrogen, Inc.).

The expression vector pcDNAI/amp contains: (1) an E. coli origin ofreplication effective for propagation in E. coli and other prokaryoticcells; (2) an ampicillin resistance gene for selection ofplasmid-containing prokaryotic cells; (3) an SV40 origin of replicationfor propagation in eukaryotic cells; (4) a CMV promoter, a polylinker,an SV40 intron; (5) several codons encoding a hemagglutinin fragment(i.e., an “HA” tag to facilitate purification) followed by a terminationcodon and polyadenylation signal arranged so that a cDNA can beconveniently placed under expression control of the CMV promoter andoperably linked to the SV40 intron and the polyadenylation signal bymeans of restriction sites in the polylinker. The HA tag corresponds toan epitope derived from the influenza hemagglutinin protein described byWilson et al., Cell 37:767 (1984). The fusion of the HA tag to thetarget protein allows easy detection and recovery of the recombinantprotein with an antibody that recognizes the HA epitope. pcDNAIIIcontains, in addition, the selectable neomycin marker.

A DNA fragment encoding the hCRY2 is cloned into the polylinker regionof the vector so that recombinant protein expression is directed by theCMV promoter. The plasmid construction strategy is as follows. The hCRY2cDNA of the deposited clone is amplified using primers that containconvenient restriction sites, much as described above for constructionof vectors for expression of hCRY2 in E. coli. Suitable primers includethe following, which are used in this example. The 5′ primer, containingthe underlined Bgl II site, a Kozak sequence, an AUG start codon and 20bases of the 5′ coding region of the hCRY2 has the following sequence:5′-GCGAGATCTCCGCCATCATGGCG-GCAACTGTGGCAAC-3′ (SEQ ID NO:14). The 3′primer, containing the underlined Xho I site, followed by 18 bp reverseand complementary to nucleotides 1822-1842 of the nucleotide sequenceset forth in SEQ ID NO:1 has the following sequence:5′-GCGCTCGAGTCAGGCATCCTTGCTCGGCCAG-3′ (SEQ ID NO:16).

The PCR amplified DNA fragment is digested with Bgl II and Xho I. Thevector, pcDNA3/Amp, is digested with BamH I and Xho I. The PCR amplifiedDNA fragment and the linearized vector are then ligated. The ligationmixture is transformed into E. coli strain SURE (available fromStratagene Cloning Systems, 11099 North Torrey Pines Road, La Jolla,Calif. 92037), and the transformed culture is plated on ampicillin mediaplates which then are incubated to allow growth of ampicillin resistantcolonies. Plasmid DNA is isolated from resistant colonies and examinedby restriction analysis or other means for the presence of thehCRY2-encoding fragment.

For expression of recombinant hCRY2, COS cells are transfected with anexpression vector, as described above, using DEAE-Dextran, as described,for instance, in Sambrook et al., Molecular Cloning: a LaboratoryManual, Cold Spring Laboratory Press, Cold Spring Harbor, N.Y. (1989).Cells are incubated under conditions for expression of hCRY2 by thevector.

Expression of the hCRY2-HA fusion protein is detected by radiolabelingand immunoprecipitation, using methods described in, for example Harlowet al., Antibodies: A Laboratory Manual, 2nd Ed.; Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1988). To this end, two daysafter transfection, the cells are labeled by incubation in mediacontaining 35S-cysteine for 8 hours. The cells and the media arecollected, and the cells are washed and lysed with detergent-containingRIPA buffer: 150 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% DOC, 50 mM TRIS, pH7.5, as described by Wilson et al. cited above. Proteins areprecipitated from the cell lysate and from the culture media using anHA-specific monoclonal antibody. The precipitated proteins then areanalyzed by SDS-PAGE and autoradiography. An expression product of theexpected size is seen in the cell lysate, which is not seen in negativecontrols.

EXAMPLE 6(b) Cloning and Expression in CHO Cells

The vector pC4 is used for the expression of hCRY2 protein. Plasmid pC4is a derivative of the plasmid pSV2-dhfr (ATCC Accession No. 37146). Theplasmid contains the mouse DHFR gene under control of the SV40 earlypromoter. Chinese hamster ovary- or other cells lacking dihydrofolateactivity that are transfected with these plasmids can be selected bygrowing the cells in a selective medium (alpha minus MEM, LifeTechnologies) supplemented with the chemotherapeutic agent methotrexate.The amplification of the DHFR genes in cells resistant to methotrexate(MTX) has been well documented (see, e.g., Alt, F. W., Kellems, R. M.,Bertino, J. R., and Schimke, R. T., J Biol. Chem. 253:1357-1370 (1978),Hamlin, J. L. and Ma, C., Biochem. et Biophys. Acta, 1097:107-143(1990), Page, M. J. and Sydenham, M. A., Biotechnology 9:64-68 (1991)).Cells grown in increasing concentrations of MTX develop resistance tothe drug by overproducing the target enzyme, DHFR, as a result ofamplification of the DHFR gene. If a second gene is linked to the DHFRgene, it is usually co-amplified and over-expressed. It is known in theart that this approach may be used to develop cell lines carrying morethan 1,000 copies of the amplified gene(s). Subsequently, when themethotrexate is withdrawn, cell lines are obtained which contain theamplified gene integrated into one or more chromosome(s) of the hostcell.

Plasmid pC4 contains for expressing the gene of interest the strongpromoter of the long terminal repeat (LTR) of the Rous Sarcoma Virus(Cullen, et al., Molecular and Cellular Biology, March 1985:438-447)plus a fragment isolated from the enhancer of the immediate early geneof human cytomegalovirus (CMV) (Boshart et al., Cell 41:521-530 (1985)).Downstream of the promoter are Bam HI, XbaI, and Asp718 restrictionenzyme cleavage sites that allow integration of the genes. Behind thesecloning sites the plasmid contains the 3′ intron and polyadenylationsite of the rat preproinsulin gene. Other high efficiency promoters canalso be used for the expression, e.g., the human β-actin promoter, theSV40 early or late promoters or the long terminal repeats from otherretroviruses, e.g., HIV and HTLVI. Clontech's Tet-Off and Tet-On geneexpression systems and similar systems can be used to express hCRY2 in aregulated way in mammalian cells (Gossen, M. and Bujard, H., Proc. Natl.Acad. Sci. USA 89: 5547-5551(1992)). For the polyadenylation of the mRNAother signals, e.g., from the human growth hormone or globin genes canbe used as well. Stable cell lines carrying a gene of interestintegrated into the chromosomes can also be selected uponco-transfection with a selectable marker such as gpt, G418 orhygromycin. It is advantageous to use more than one selectable marker inthe beginning, e.g., G418 plus methotrexate.

The plasmid pC4 is digested with the restriction enzymes BamH I and XbaI and then dephosphorylated using calf intestinal phosphatase byprocedures known in the art. The vector is then isolated from a 1%agarose gel.

The DNA sequence encoding the complete hCRY2 protein including itsleader sequence is amplified using PCR oligonucleotide primerscorresponding to the 5′ and 3′ sequences of the gene. The 5′ primer hasthe sequence 5′-GCGAGATCTCCGCCATCATGGCGGCAACTGTGGCAAC-3′ (SEQ ID NO:14)containing the underlined Bgl II restriction enzyme site followed by anefficient signal for initiation of translation in eukaryotes, asdescribed by Kozak, M., J. Mol. Biol. 196:947-950 (1987), and 22 basescorresponding to nucleotides −2 to 20 of SEQ ID NO:1. The 3′ primer hasthe sequence 5′-GCGTCTAGATCAGGCATCCTTGCTCGG-3′ (SEQ ID NO:15),containing the underlined Xba I restriction site followed by a stopcodon and 18 nucleotides reverse and complementary to nucleotide1825-1842 in the sequence set forth in SEQ ID NO:1.

The amplified fragment is digested with the endonucleases Bgl II and XbaI and is then purified again on a 1% agarose gel. The isolated fragmentand the dephosphorylated vector are then ligated with T4 DNA ligase. E.coli H13101 or XL-1 Blue cells are then transformed and bacteria areidentified that contain the fragment inserted into plasmid pC4 using,for instance, restriction enzyme analysis.

Chinese hamster ovary cells lacking an active DHFR gene are used fortransfection. 5 μg of the expression plasmid pC4 is cotransfected with0.5 μg of the plasmid pSV2-neo using lipofectin (Felgner et al., supra).The plasmid pSV2neo contains a dominant selectable marker, the neo genefrom Tn5 encoding an enzyme that confers resistance to a group ofantibiotics including G418. The cells are seeded in alpha minus MEMsupplemented with 1 mg/ml G418. After 2 days, the cells are trypsinizedand seeded in hybridoma cloning plates (Greiner, Germany) in alpha minusMEM supplemented with 10, 25, or 50 ng/ml of methotrexate plus 1 mg/mlG418. After about 10-14 days, single clones are trypsinized and thenseeded in 6-well petri dishes or 10 ml flasks using differentconcentrations of methotrexate (50 nM, 100 nM, 200 nM, 400 nM, 800 nM).Clones growing at the highest concentrations of methotrexate are thentransferred to new 6-well plates containing even higher concentrationsof methotrexate (1 μM, 2 μM, 5 μM, 10 mM, 20 mM). The same procedure isrepeated until clones are obtained which grow at a concentration of100-200 μM. Expression of the desired gene product is analyzed, forinstance, by SDS-PAGE and Western blot or by reverse phase HPLCanalysis.

EXAMPLE 7 Tissue Distribution of hCRY2 mRNA Expression

Northern blot analysis was carried out to examine hCRY2 gene expressionin human tissues, using methods described by, among others, Sambrook etal., cited above. A cDNA probe containing the entire nucleotide sequenceof the hCRY2 protein (SEQ ID NO:1) was labeled with ³²p using theRediprime™ DNA labeling system (Amersham Life Science, Arlington, Ill.),according to manufacturer's instructions. After labeling, the probe waspurified using a CHROMA SPIN-100™ column (Clontech Laboratories, Inc.),according to manufacturer's protocol number PT1200-1. The purifiedlabeled probe was then used to examine various human tissues for hCRY2mRNA.

Multiple Tissue Northern (MTN) blots containing various human tissueswere obtained from Clontech and were examined with the labeled probeusing ExpressHyb™ hybridization solution (Clontech) according tomanufacturer's protocol number PT1190-1. Following hybridization andwashing, the blots were mounted and exposed to film at −70° C.overnight, and films developed according to standard procedures.

Multiple, stronger signals, ranging size from about 1.4 to greater thanabout 9.5 kB, were detected in lanes corresponding to RNA from heart,brain, skeletal muscle, and pancreas. Weaker signals, ranging in sizefrom about 1.4 to about 4 kb were detected in lanes corresponding tolung and kidney.

It will be clear that the invention may be practiced otherwise than asparticularly described in the foregoing description and examples.

Numerous modifications and variations of the present invention arepossible in light of the above teachings and, therefore, are within thescope of the appended claims.

The entire disclosure of all publications (including patents, patentapplications, journal articles, laboratory manuals, books, or otherdocuments) cited herein are hereby incorporated by reference.

1. An isolated antibody that specifically binds a protein selected fromthe group consisting of: (a) a protein consisting of amino acid residues191 to 571 of SEQ ID NO:2; (b) a protein consisting of amino acidresidues 1 to 492 of SEQ ID NO:2; (c) a protein consisting of amino acidresidues ito 571 of SEQ ID NO:2; and, (d) a protein consisting of aminoacid residues −22 to 571 of SEQ ID NO:2.
 2. The antibody of claim 1 thatspecifically binds protein (a).
 3. The antibody of claim 1 thatspecifically binds protein (b).
 4. The antibody of claim 1 thatspecifically binds protein (c).
 5. The antibody of claim 1 thatspecifically binds protein (d).
 6. The antibody of claim 1 thatspecifically binds protein (c).
 7. The antibody of claim 1 which is amonoclonal antibody.
 8. A method of detecting human blue-lightphotoreceptor hCRY2 (hCRY2) protein in a biological sample comprising:(a) contacting the biological sample with the antibody of claim 1; (b)allowing a complex to form between said hCRY2 protein and said antibodyof claim 1; and (c) detecting said complex.
 9. An isolated antibody thatspecifically binds to a protein selected from the group consisting of:(a) a protein consisting of the mature polypeptide encoded by the cDNAclone contained in ATCC Deposit Number 97769; and, (b) a proteinconsisting of the complete polypeptide encoded by the cDNA clonecontained in ATCC Deposit Number
 97769. 10. The antibody of claim 9 thatspecifically binds protein (a).
 11. The antibody of claim 9 thatspecifically binds protein (b).
 12. The antibody of claim 10 thatspecifically binds protein (b).
 13. The antibody of claim 9 which is amonoclonal antibody.
 14. A method of detecting hCRY2 protein in abiological sample comprising: (a) contacting the biological sample withthe antibody of claim 9; (b) allowing a complex to form between saidhCRY2 protein and said antibody of claim 9; and, (c) detecting saidcomplex.
 15. An isolated antibody that specifically binds a hCRY2protein expressed on the surface of a cell wherein said cell comprises apolynucleotide encoding amino acids 1 to 571 of SEQ ID NO:2 operativelylinked with a regulatory sequence that controls the expression of saidpolynucleotide, and further wherein said hCRY2 protein is encoded bysaid polynucleotide.
 16. The antibody of claim 15 which is a monoclonalantibody.
 17. The antibody of claim 15, wherein said cell is a mammaliancell.
 18. The antibody of claim 15, wherein said cell is a ChineseHamster Ovaxy (CHO) cell.
 19. An isolated antibody that specificallybinds a hCRY2 protein expressed on the surface of a cell wherein saidcell comprises a polynucleotide having a polynucleotide sequence of theCDNA clone contained in ATCC Deposit 97769 wherein said polynucleotideis operatively linked with a regulatory sequence that controls theexpression of said polynucleotide, and further wherein said hCRY2protein is encoded by said polynucleotide.
 20. The antibody of claim 19which is a monoclonal antibody.
 21. The antibody of claim 19, whereinsaid cell is a mammalian cell.
 22. The antibody of claim 19, whereinsaid cell is a Chinese Hamster Ovary (CHO) cell.